Try hooking DVD player right to the TV and bypass the Yamaha.
I wonder if it could be different versions of HDMI?
According to the Sony web site it does up-convert to 1080p?
http://www.sonystyle.com/webapp/wcs/stores/servlet/ProductDisplay?catalogId=10551&storeId=10151&productId=8198552921665393601&langId=-1
I agree with the suggestion in your first sentence and believe that your postulation in your second is quite possible.
As for it upconverting to 1080p, I must ask why this is a priority. First off,the only source of "true" 1080p viewing is the two previously mentioned HD video formats, and these need no upconversion. Standard DVd's are still 480 and always will be.
All Televisions "upconvert" internally into it's best native resolution. By forcing this issue in upstream components presupposes that they can do a better job than the TV. This isn't always the case and, with HDMI "standards" in such flux, it seems that it may actually create more problems than it solves.
And, while the DVD player may upconvert the 480 of a standard DVD to output 1080p at the HDMI output (I didn't look), it won't really "improve" the picture significantly. The TV might do a better job and that's why your first sentence makes so much sense.
Additionally, if the DVD player (at 1080p) works correctly when connected to the TV, it will narrow down a sitiation with the reeiver. If not, it will point to a situation with either the DVD player or the TV itself. That can become trickier. but, one step at a time.